Table 1.

Comparison of major features of methods developed for cross species expression analysis

	Coexpression meta-analysis (metagene, signature algorithm)	Expression meta-analysis (raw aggregation, P-value)	Indirect (GSEA)	Single species arrays	Multi-species arrays	Combined analysis (MRF)
Single platform for all experiments	No	No	No	Yes	Yes	No
Customized array	No	No	No	No	Yes	No
Similar experimental conditions	No	Yes	Yes	Yes	Yes	Yes
Directly compares expression profiles	No	No	No	Yes	Yes	Yes
Can be applied to distant species	Yes	Yes	Yes	No	No	Yes
Requires orthology information	Yes	Yes	Yes	No	Yes	No
Separate P-value cut-off for each species	No	Yes	Yes	No	No	No